Method for selecting cancer treatment regimen

ABSTRACT

Disclosed is a method for selecting a cancer treatment regimen for a subject.

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims benefit of priority to U.S. ProvisionalApplication No. 61/904,550, filed Nov. 15, 2013, which is herebyincorporated herein by reference in its entirety.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with Government Support under Grant No. CA143803and Grant No. CA164322 awarded by the National Institutes of Health. TheGovernment has certain rights in the invention.

BACKGROUND

The purposes of pre-clinical systems range from early identification ofcompounds with anti-cancer activity, estimation of patient-specificclinical response, or the discovery of novel targetable cellularmechanisms (Suggitt M, Bibby MC. Clinical Cancer Research2005;11:971-81; Von Hoff DD, Clark GM, et al. Cancer Res1983;43:1926-31). All available systems have strengths and limitations:in vitro assays using cell lines are scalable, reproducible andinexpensive, but cell lines are significantly different from theiroriginating tumors (Pellat-Deceunynk C, Amiot M, et al. Blood1995;86:4001-2), and the tumor microenvironment’s effects are oftenabsent in these assays. Animal models include more realistic elementssuch as drug pharmacokinetics and influence of the tumormicroenvironment, but they often rely on cell lines, require long-termexperiments, and carry significant financial cost. Irrespective of thepre-clinical model used, the data generated cannot be directly portedinto clinical estimations without the help of an adequate computationalframework.

Computational modeling has long been used to study the dynamics of tumorresponse to therapy, as well as emergence of drug resistance (HokansonJA, Brown BW, et al. Cancer 1977;39:1077-84; Chmielecki J, Foo J, et al.Sci Transl Med 2011;3:90ra59; Tang M, Gonen M, et al. Blood2011;118:1622-31). These theoretical models are powerful tools foranalyzing complex interactions like the tumor-host-therapy system, andcould, in a near future, become decision-support systems foroncologists, making personalized oncology a possibility (Gardner SN,Fernandes M. Mol Cancer Ther 2003;2:1079-84). The Achilles’ heel of suchmodels, however, is the reliability of the experimental data used toparameterize them. More often than not, these computational models areparameterized by data from literature, in many cases from experimentsthat have been performed at incompatible conditions.

Four decades ago, Salmon and collaborators (Salmon SE, Hamburger AW, etal. N Engl J Med 1978;298:1321-7) proposed an in vitro method forestimation of clinical response of cancer patients based on the capacityof primary cancer cells to form colonies at physiologically reachablechemotherapy concentrations. The main limitation of these early assays,however, was the small number of patient samples that were capable offorming colonies under control conditions. With a cloning efficiencybetween 0.001% and 0.1%, the growth of colonies in vitro was a challengecomparable to surviving the chemotherapeutic insult itself.Consequently, these restrictions limited the number of drugs,concentrations and time points that could be studied for a singlepatient (Suggitt M, Bibby MC. Clin Cancer Res 2005;11:971-81), even inmore recent models (Kirshner J, Thulien KJ, et al. Blood2008;112:2935-4). Finally, the outcome of these assays were oftendichotomized, in other words, either a patient was “sensitive” or“resistant” to the drug, but no information was provided regardingduration of response and time to relapse. Given that in many cancers theoverall survival is more dependent on the duration of the response thanon its depth (Durie BG, Jacobson J, et al. J Clin Oncol 2004;22:1857-63;Harousseau JL, Attal M, Avet-Loiseau H. Blood 2009;114:3139-46), theapplication of these early assays as predictive biomarkers was somewhatlimited.

The methods disclosed herein address these and other limitations.

SUMMARY

Disclosed herein are non-destructive methods for quantifying cellviability. In some examples, the method can comprise culturing aplurality of cells from a subject in a chamber; capturing a firstoptical signal from the cells at a first time point; capturing a secondoptical signal from the cells at a second time point; analyzing thefirst optical signal and the second optical signal to detect cellmembrane motion of the cells; and analyzing the cell membrane motion toquantify the viability of the cells. In some embodiments, the method isused to quantify cell viability after the cells have been contacted withan active agent.

Any cell type can be assayed by the disclosed methods. For example, themethods can be used to test for toxicity of a candidate agent on normalcells. Alternatively, the methods can be used to test cytotoxicity of adrug on abnormal cells, such as an antineoplastic drug on cancer cells.Therefore, in some examples, the cells are cancer cells, which caninclude solid tumor cells or hematological cancer cells (e.g., multiplemyeloma).

The chamber of the disclosed method can be any chamber suitable toculture cells and allow imaging of the cells while in culture. Forexample, in some examples, the chamber is a microfluidic chamber. Insome examples, the chamber is a well in a multiwell-plate.

In some examples, the chamber can recapitulate the cell’s naturalmicroenvironment. This can involve the use of growth media, polymersubstrates, feeder cells, stromal cells, growth factors, and the like.In some cases, the chamber recapitulates a cancer microenvironment. Forexample, culturing hematological cancer cells can involve a 3Dreconstruction of the cancer microenvironment, e.g., including primaryhematological cancer cells, extracellular matrix, patient-derivedstroma, and growth factors.

In some examples, the active agent can comprise an anticancer agent,such as a chemotherapeutic agent. In some examples, the active agent cancomprise a combination of active agents. For example, the anticanceragent can be a composition comprising melphalan, bortezomib, FAM-HYD-1,Marizomib (NPI-0052), Carfilzomib, Cytoxan, Dexamethasone, Thalidomide,Lenalidomide, Oprozomib, Panobinostat, Quisinostat, and Selinexor, orany combination thereof.

In some examples, the first optical signal, the second optical signal,or a combination thereof involves any optical microscopy illuminationtechniques suitable to detect cell membrane activity, such as a brightfield illumination, dark field illumination, and phase contrastillumination.

In some examples, the cells of the method are obtained by collecting asample from the subject and then isolating the cells from the sample. Asan example, the sample can comprise a bone marrow aspirate where thecells are hematological cancer cells isolated from the aspirate, e.g.,by flow cytometry using a cell surface cancer marker.

In some examples, the method can further comprise collecting parametersfrom the viability observations to generate a multi-parameter model thatsummarizes the response of a cancer in a subject to the active agent.

Also disclosed herein are methods for predicting a response of a subjectto treatment with an active agent. The methods can comprise firstpreparing a three-dimensional dose-response curve by assessing theviability of cells from the subject in response to the active agent at aplurality of time points at a plurality of dosages. The method can theninvolve generating a multi-parameter model that summarizes thethree-dimensional dose-response curve. The multi-parameter model canthen be used to calculate the rate of accumulation of damage in thecells due to the active agent and the active agent-induced cell deathdue to the accumulated damage. In some embodiments, the number ofdistinct populations in the cells is a covariate in the multi-parametermodel, so the method can involve determining the number of populations.The rate of accumulation of damage in the cells and the activeagent-induced cell death due to the accumulated damage can then beextrapolated to predict a response of the subject to the active agent.For example, a three-dimensional dose-response curve based on 2, 3, 4,5, 6, 7 days of viability data can be extrapolated to 1, 2, 3, 4, 5, 6,7, 8, 9, 10, or more years of response by the subject.

In some examples, the methods disclosed herein can further compriseselecting a cancer treatment regimen for the subject based on predictedresponses to 2, 3, 4, 5, 6, 7, 8, 9, 10, or more different activeagents.

In some examples, the method can predict an initial response of thesubject to the active agent. In some examples, the method can predictthe chance of progression-free survival. In some examples, the methodcan predict the chance of developing environment-mediated resistance tothe active agent. In some examples, the method can predict an effectivedosing schedule of the active agent. In some examples, the method canpredict an effective concentration of the active agent.

Also disclosed herein are platforms to study drug response in cancer. Inparticular, methods for selecting a cancer treatment regimen for asubject are disclosed. The method can first involve administering cancercells from the subject to a chamber that recapitulates the cancermicroenvironment. For example, the chamber can contain 3D extracellularmatrix and mesenchymal cells derived from the tumor microenvironment.The chamber can further contain the drug to be tested present in alinear gradient across the chamber. The method can then involvedetecting cell death induced by the drug across the drug gradient at oneor more time points. These and other parameters collected from the assaycan then be used to generate a multi-parameter model that summarizes theresponse of the subject to the drug treatment. This is preferably doneusing computational modeling. The method can be used to select a cancertreatment regimen for the subject based on the results of themulti-parameter model.

The details of one or more embodiments of the invention are set forth inthe accompanying drawings and the description below. Other features,objects, and advantages of the invention will be apparent from thedescription and drawings, and from the claims.

DESCRIPTION OF DRAWINGS

FIG. 1 : Schematic view of microfluidic assay used for in vitroreconstruction of bone marrow. (1) Each microfluidic chip containedthree chambers, each of them composed of two side reservoirs, and onecenter observation chamber. Myeloma and stromal cells were loaded in theobservation chamber simultaneously, resuspended in collagen. Overnight,the matrix gellifies, and stromal cells adhered to the bottom of thechamber and stretch. (2) One of the side reservoirs was filled withmedium with a chemotherapeutic agent (left), while the other was filledwith standard growth medium (right). The diffusion of thechemotherapeutic agent from one reservoir to the other created a stablegradient across the observation chamber. (3) The observation channelwith the human MM cell line NCI-H929 and adherent bone marrow derivedstromal cell line HS-5 is shown in bright field under a gradient of thenecrosis-inducing peptide HYD-1. Note that MM cells on the left (higherdrug concentration) have died and became dark spots, while cells on theright (lower drug concentration) are still alive. (4) A gradient of thefluorescent conjugated peptide FAM-HYD1 was established, andfluorescence quantified across the channel during 18 h. Normalizationand re-scaling to the minimum and maximum concentration within theobservation channel confirm the linear stable gradient during the 18 hwindow of experiment.

FIG. 2 : Loss of membrane motion precedes loss of innate fluorescence inMM fluorescent cell line. The cell line RMPI-8226 was stably transfectedwith the fluorescent protein dsRed2. Upon death, cells stop producingthe protein, which can degrade inside the cytoplasm and/or diffuse tomedia upon cell membrane bursting. FIG. 2 depicts four examples of thesecells exposed to 50 µM melphalan for 24 h. The first column depicts theinitial time point, when all cells are alive. The red fluorescentchannel was superimposed to the transmitted light, while the motiondetection algorithm pseudo-colored them as green. The second columnshows the moment of loss of membrane motion, while the third columnshows the moment of loss of red fluorescence. The last column representsthe last time point, when Calcein AM was added to identify live cells.

FIG. 3 : Loss of membrane motion is an early event in cell death,preceding loss of membrane integrity. FIG. 3 shows four examples ofH929/S cells exposed to a stable drug gradient of Melphalan, from 50 to10 µM. At the beginning of the experiment, all live cells werepseudo-colored in green from motion detection. The moment of loss ofmembrane motion was marked by the disappearance of green in the image.There was a variable delay between loss of membrane motion andacquisition of red fluorescence, which is a combination of loss ofmembrane integrity and binding of EthD-1 to DNA.

FIG. 4 : Quantification of sensitivity of the human myeloma cell lineNCI-H929 to the proteasome inhibitor bortezomib. The disclosedmicrofluidic assay was used to generate a series of measurementscorresponding to cell viability at combination of exposure time and drugconcentration. These data points in turn were fit to the mathematicalexpression of dose response, Equation 1. (A) Sensitivity of the humanmyeloma cell line to the proteasome inhibitor bortezomib. (B) Goodnessof fit of the mathematical model to the 1,670 data points. (C)Comparison of viability measurements at 24 h between the mathematicalmodel and a standard ATP-based bioluminescent assay, with NCI-H929 cellsin suspension in media or in collagen, using a standard 96-well plate.

FIG. 5 : Intrinsic chemoresistance to melphalan. The human MM cell lines8226/LR5, selected by continuous exposure to melphalan, and NCI-H929were exposed for a 24 h continuous stable of gradient of melphalan inthe microfluidic chamber. While the cell line NCI-H929 was fit to asingle population, the 8226/LR5 cell line was better fit by atwo-population curve, with approximately 70% of resistant cells and 30%of sensitive. This result indicates that the loss of chemoresistance of8226/LR5 cells in absence of melphalan might be due to heterogeneity inthis population.

FIG. 6 : The duration of melphalan toxicity post-withdrawal. 8226/LR5(top) and NCI-H929 (bottom) cells were exposed to a melphalan gradientwith highest concentration of 20 µM. Melphalan’s half-life isapproximately 1-2 h in media. At highest concentration, NCI-H929 cellsbegan to die after 24 h, while 8226/LR5 viability began to decline at36h. Both cell lines continued dying for over a week. This delayedtoxicity of melphalan was thus considered in the computational model forclinical response (Equation 2).

FIG. 7 : Effect of Cell Adhesion Mediated Drug Resistance in the MM cellline NCI-H929 treated with melphalan. (Top) The co-culture of theNCI-H929 human MM cell line with the human bone marrow derived stromalcell line HS-5 confers increased resistance to melphalan. Melphalanconcentration and exposure used to reduce viability in 50% (kR and kT,respectively) increase from 28 to 40 µM and 12 to 15 h, respectively.(Bottom) Linear regression of fit and actual experimental points forboth experiments.

FIG. 8 : The duration of bortezomib activity post-withdrawal. NCIH929cells in two microfluidic chambers were exposed to a bortezomib gradientfor 24 h. After 24 h, the media from both chambers were replaced. Drugwas refreshed in the first chamber (top), while drug was removed fromthe second (bottom, P, for pulsed exposure). As shown in the 65h-study,upon removal of bortezomib, cell death stops and cells resume growth.Same assay could be used to study lingering effects of experimentaldrugs with short half-lives.

FIG. 9 : Primary MM cells in co-culture with patient stroma aresignificantly more resistant to melphalan. Patient 14 was a newlydiagnosed patient. MM cells were sorted (CD138+) from bone marrowaspirate, and seeded into microfluidic chamber in single (SCX, 0h) orco-culture with patient stromal cells (CoCx, 0 h). Digital imageanalysis identified live cells and pseudo-colored them as green. Astable linear gradient of melphalan was established across observationchannel: 25 µM on the left, 0 µM on the right, and cells were imagedevery 5 minutes for 48 h. After 48 h, almost all MM cells were dead insingle culture (SCX, 48 h), while a significant number of MM cells werestill alive in co-culture with stroma (CoCx, 48 h). (A) Dose responsesurfaces built using measurements of viability in single (SCX) andco-culture (CoCx). (B) Goodness of fit of dose response surfaces (model)and actual data points for single culture, and (C) co-culture.

FIG. 10 : Quantification of bortezomib-induced EMDR circumvention inprimary MM cells. Patient 14 was a newly diagnosed patient. MM cellswere sorted (CD138+) from bone marrow aspirate, and seeded intomicrofluidic chamber in single and co-culture with adherent stromalcells (CD138-). (A) In single culture, MM cells were significantly moresensitive than in co-culture (B). A dose-response assay with bortezomibindicated that 1 nM was the highest concentration that did not cause MMcell death (C) during the 24 h-period. By combining a stable gradient ofmelphalan, with a uniform concentration of bortezomib, thechemosensitive phenotype is restored in co-culture (D).

FIG. 11 : In vitro melphalan chemosensitivity of three MM patients.Patient 14 was a newly diagnosed/high-risk patient, patient 12 was arelapsed/standard risk patient previously treated with high-dosemelphalan and bone marrow transplantation. Patient 11 was asmoldering/standard-risk patient. In all three assays, cells were seededin single culture in 3D collagen matrix with patient plasma supplementedmedium. (Top, left) After 24 h continuous exposure to a stable melphalangradient ranging from 0 to 50 µM, cells from the three patientsresponded at different rates, with patient 12 being the most resistant,and patient 11 the most sensitive. While the EC₅₀ for 24h (Top, right)was approximately 4 µM for patients 12 and 14, and approximately 1 µMfor patient 11, the EC₂₀, for example, was significantly higher in therelapsed patient: 50 µM for patient 12, 10 µM for patient 14, andapproximately 3 µM for patient 11.

FIG. 12 : In vitro response of primary MM cells to bortezomib in singleculture 3D collagen matrix. Patient 11 was a smoldering/standard-riskpatient, and thus never previously treated with bortezomib. Patient 12was a relapsed/standard-risk patient previously treated withbortezomib-based regimens, and high-dose melphalan followed by bonemarrow transplantation. Patient 12′s bortezomib-based induction regimen(bortezomib/lenalidomide/dexamethasone) occurred 3 years prior to thebiopsy used for this in vitro assay. Patient 13 was a newlydiagnosed/high-risk patient, while patient 17 was a smoldering myelomapatient.

FIG. 13 : Computational modeling of in vivo response to therapy. Byparameterizing Equation 3 with the dose response constants obtained fromNCI-H929 cells exposed to a bortezomib gradient (FIG. 2 ), it waspossible to simulate how a bi-weekly treatment of a subcutaneous SCIDmouse model would affect tumor growth. Pearson’s correlation “r value”was 0.9869 (P=0.0003) between actual measurements (Ishii T, Seike T, etal. Blood Cancer J 2012;2) and simulated tumor burden under a 1 mg/kgbi-weekly bortezomib regimen, which leads to a stable concentration of~0.4 nM bortezomib in plasma (Williamson MJ, Silva MD, et al. Mol CancerTher 2009;8:3234-43). Using the same computational model, it waspossible to test hypothetical treatments, such as, for instance, aregimen with holidays where the double of the amount of bortezomib wouldbe administered every other week (0.8 nM w/ holidays).

FIG. 14 : Computational modeling of clinical response to therapy. Theparameters of bortezomib chemosensitivity obtained in vitro from fourpatients (FIG. 7 ) were used in Equation 3 to simulate how thesepatients would have responded to a single agent bortezomib hypotheticaltreatment. The regimen simulated was 1.3 mg/m² doses on days 1, 4, 8,and 11, leading to a stable plasma concentration of approximately 1 nM(Reece DE, Sullivan D, et al. Chemother Pharmacol 2011;67:57-67).

FIG. 15 : Schematic view of multiwell assay. During a standard-of-carebone marrow biopsy, an extra volume of 10 mL of aspirate was taken forresearch. The cancer cells were separated from non-cancer by magneticbead sorting (antibody for CD138, a marker of MM cells). Cancer cellsfrom the patient were re-suspended in colagen I or matrigel or any othermatrix of choice in conjunction with stromal cells (adherent non-cancercells obtained from bone marrow biopsies, CD138-) (A). This cell-matrixmix was seeded in multi-well plates and left to polymerize overnight.During this process the stromal cells adhere to the bottom of the wellswhile MM cells remain in suspension (B). The wells are organized so thatmultiple drugs can be tested, each at a number of differentconcentrations (e.g., 5) and in different number of replicates (e.g., 2or more). By imaging at regular intervals each well in bright field, andusing a digital image analysis algorithm (FC), live and dead cells weredetected non-destructively at each well (D). The replicates were thencombined and the results for each drug were clustered, normalized by thecontrols (no drugs added) and the dose-response curves were built (E).

FIG. 16 : Schematic of an example multiwell plate. In this example, onesample from a patient (wells in columns 2-8 and rows B-L) was tested forsensitivity to 7 drugs: melphalan (MEL), carfilzomib (CFZ),dexamethasone (DEX), doxorubicin (a.k.a. Adriamycin, ADR), Selinexor(KPT), Panobinostat (PAN) and Quisinostat (QST). The highestconcentrations of drug were on row ‘B’ and are serially diluted 3-foldevery row from ‘C’ to ‘F’, thus 5 different drug concentrations for eachdrug. The same pattern was repeated from line ‘H’ until ‘L’,representing the second replicate. Squares 114-117 represent thecontrols: the cells in these wells did not receive any drug. Theconcentrations in row ‘M’ are the highest concentration for each drug inthe panel. In the same plate, a second experiment was performed toassess how the microenvironment can affect drug efficacy. For thisexperiment, a multiple myeloma cell line in co-culture with mesenchymalstem cells in collagen matrix (columns 10-16, rows B-E and columns 11and 12 on row G), in single culture in collagen matrix (columns 12, 13,20, and 21 on row G, and columns 10-16 and 18-24 on rows H-L) and insingle culture in media (Columns 18-24, rows B-F, and columns 18 and 19on row G) were used.

FIG. 17 : Example of the model implementation. (A) The dose-responsecurves for each patient and each drug were fit to (B) a computationalmodel that describes the rate of accumulation of damage due to drugexposure as well as drug-induced cell death due to accumulated damage.The patient-specific model can be represented by one population(perfectly homogeneous tumor), two populations or three populations. (Cand D) Pearson’s correlation of these three hypotheses were computed,and the model with fewest populations and best fit (highest r^2) wasselected.

FIG. 18 : Dose-response curve for Patient 6 and Marizomib (NPI-0052). Aselected patent-specific model was simulated in a clinical regimen ofthe drug, and two estimates are made: “best case” scenario (ModelM-Spike Max) and “worst case” scenario (Model M-Spike Min). In the“worst case” scenario the growth rate is 1% for newly diagnosed patientsand the highest previous growth rate of the tumor for relapsed patients,based on prior clinical data. In the “best case” scenario the growthrate of the tumor is zero for newly diagnosed patients and the minimumbetween 1% and “worst case” rate for relapsed patients.

FIG. 19 : Dose-response curve for Patient 7 and a drug combination ofCarfilzomib, Cytoxan and Dexamethasone. A selected patent-specific modelwas simulated in a clinical regimen of the drug, and two estimates aremade: “best case” scenario (Model M-Spike Max) and “worst case” scenario(Model M-Spike Min). In the “worst case” scenario the growth rate is 1%for newly diagnosed patients and the highest previous growth rate of thetumor for relapsed patients, based on prior clinical data. In the “bestcase” scenario the growth rate of the tumor is zero for newly diagnosedpatients and the minimum between 1% and “worst case” rate for relapsedpatients.

FIG. 20 : Dose-response curve for Patient 9 and Marizomib (NPI-0052). Aselected patent-specific model was simulated in a clinical regimen ofthe drug, and two estimates are made: “best case” scenario (ModelM-Spike Max) and “worst case” scenario (Model M-Spike Min). In the“worst case” scenario the growth rate is 1% for newly diagnosed patientsand the highest previous growth rate of the tumor for relapsed patients,based on prior clinical data. In the “best case” scenario the growthrate of the tumor is zero for newly diagnosed patients and the minimumbetween 1% and “worst case” rate for relapsed patients.

FIG. 21 : Dose-response curve for Patient 10 and a drug combination ofCarfilzomib, Thalidomide (Thali), and Dexamethasone. A selectedpatent-specific model was simulated in a clinical regimen of the drug,and two estimates are made: “best case” scenario (Model M-Spike Max) and“worst case” scenario (Model M-Spike Min). In the “worst case” scenariothe growth rate is 1% for newly diagnosed patients and the highestprevious growth rate of the tumor for relapsed patients, based on priorclinical data. In the “best case” scenario the growth rate of the tumoris zero for newly diagnosed patients and the minimum between 1% and“worst case” rate for relapsed patients.

FIG. 22 : Dose-response curve for Patient 11 and a drug combination ofBortezomib (V) and Dexamethasone (D). A selected patent-specific modelwas simulated in a clinical regimen of the drug, and two estimates aremade: “best case” scenario (Model M-Spike Max) and “worst case” scenario(Model M-Spike Min). In the “worst case” scenario the growth rate is 1%for newly diagnosed patients and the highest previous growth rate of thetumor for relapsed patients, based on prior clinical data. In the “bestcase” scenario the growth rate of the tumor is zero for newly diagnosedpatients and the minimum between 1% and “worst case” rate for relapsedpatients.

FIG. 23 : Dose-response curve for Patient 12 and a drug combination ofBortezomib (V), Lenalidomide (R), and Dexamethasone (D). A selectedpatent-specific model was simulated in a clinical regimen of the drug,and two estimates are made: “best case” scenario (Model M-Spike Max) and“worst case” scenario (Model M-Spike Min). In the “worst case” scenariothe growth rate is 1% for newly diagnosed patients and the highestprevious growth rate of the tumor for relapsed patients, based on priorclinical data. In the “best case” scenario the growth rate of the tumoris zero for newly diagnosed patients and the minimum between 1% and“worst case” rate for relapsed patients.

FIG. 24 : Dose-response curve for Patient 14 and a drug combination ofBortezomib (V) and Dexamethasone (D). A selected patent-specific modelwas simulated in a clinical regimen of the drug, and two estimates aremade: “best case” scenario (Model M-Spike Max) and “worst case” scenario(Model M-Spike Min). In the “worst case” scenario the growth rate is 1%for newly diagnosed patients and the highest previous growth rate of thetumor for relapsed patients, based on prior clinical data. In the “bestcase” scenario the growth rate of the tumor is zero for newly diagnosedpatients and the minimum between 1% and “worst case” rate for relapsedpatients.

FIG. 25 : Dose-response curve for Patient 15 and a drug combination ofBortezomib (V), Lenalidomide (R), and Dexamethasone (D). A selectedpatent-specific model was simulated in a clinical regimen of the drug,and two estimates are made: “best case” scenario (Model M-Spike Max) and“worst case” scenario (Model M-Spike Min). In the “worst case” scenariothe growth rate is 1% for newly diagnosed patients and the highestprevious growth rate of the tumor for relapsed patients, based on priorclinical data. In the “best case” scenario the growth rate of the tumoris zero for newly diagnosed patients and the minimum between 1% and“worst case” rate for relapsed patients.

FIG. 26 : Dose-response curve for Patient 18 and a drug combination ofOprozomib and Dexamethasone. A selected patent-specific model wassimulated in a clinical regimen of the drug, and two estimates are made:“best case” scenario (Model M-Spike Max) and “worst case” scenario(Model M-Spike Min). In the “worst case” scenario the growth rate is 1%for newly diagnosed patients and the highest previous growth rate of thetumor for relapsed patients, based on prior clinical data. In the “bestcase” scenario the growth rate of the tumor is zero for newly diagnosedpatients and the minimum between 1% and “worst case” rate for relapsedpatients.

FIG. 27 : Dose-response curve for Patient 21 and Bortezomib. A selectedpatent-specific model was simulated in a clinical regimen of the drug,and two estimates are made: “best case” scenario (Model M-Spike Max) and“worst case” scenario (Model M-Spike Min). In the “worst case” scenariothe growth rate is 1% for newly diagnosed patients and the highestprevious growth rate of the tumor for relapsed patients, based on priorclinical data. In the “best case” scenario the growth rate of the tumoris zero for newly diagnosed patients and the minimum between 1% and“worst case” rate for relapsed patients.

FIG. 28 : Pearson correlation between actual and model predictions fornormalized tumor burden measurements for 10 MM patients treated withproteasome inhibitor-based regimens at Moffitt Cancer Center. The dashedsquare shows that all patients for whom the model predicted a clinicalresponse, actually responded, and all those predicted not to have aresponse indeed did not respond. Different filled in circles representthe interval of time after biopsy when each tumor measurement of made:less than a month (light grey), between one and two months (white), andover two months (dark grey).

FIG. 29 : Actual and estimated normalized tumor burden for multiplemycloma patients treated in proteasome inhibitor-based regimens. 10multiple myeloma patients who donated bone marrow aspirates for theassay described herein were followed after treatment. Each entry in thecolumn ‘Time (months)’ represents the delay (in months) between thetumor burden measurement and the original biopsy. Column ‘ClinicalBurden (% original)’ represents the tumor burden measurement at thatparticular moment in time normalized by the tumor burden at the time ofbiopsy. ‘Mean’ is the average between the model estimations for best(‘Min’) and worst (‘Max’) case scenarios, which correspond to smallestand largest tumor estimation. ‘Treatment’ represents the actual clinicaltreatment received by the patient. ‘Drug Ex vivo’ represents the drugused to test the sensitivity of the cells of these patients and createthe estimations of clinical response.

FIG. 30 : Schematic of an exemplary computing device.

DETAILED DESCRIPTION

The methods described herein may be understood more readily by referenceto the following detailed description of specific aspects of thedisclosed subject matter and the Examples and Figures included therein.

Before the present methods are disclosed and described, it is to beunderstood that the aspects described below are not limited to specificsynthetic methods or specific reagents, as such may, of course, vary. Itis also to be understood that the terminology used herein is for thepurpose of describing particular aspects only and is not intended to belimiting.

Also, throughout this specification, various publications arereferenced. The disclosures of these publications in their entiretiesare hereby incorporated by reference into this application in order tomore fully describe the state of the art to which the disclosed matterpertains. The references disclosed are also individually andspecifically incorporated by reference herein for the material containedin them that is discussed in the sentence in which the reference isrelied upon.

General Definitions

In this specification and in the claims that follow, reference will bemade to a number of terms, which shall be defined to have the followingmeanings:

Throughout the description and claims of this specification the word“comprise” and other forms of the word, such as “comprising” and“comprises,” means including but not limited to, and is not intended toexclude, for example, other additives, components, integers, or steps.

As used in the description and the appended claims, the singular forms“a,” “an,” and “the” include plural referents unless the context clearlydictates otherwise. Thus, for example, reference to “a composition”includes mixtures of two or more such compositions, reference to “anagent” includes mixtures of two or more such agents, reference to “thecomponent” includes mixtures of two or more such components, and thelike.

“Optional” or “optionally” means that the subsequently described eventor circumstance can or cannot occur, and that the description includesinstances where the event or circumstance occurs and instances where itdoes not.

Ranges can be expressed herein as from “about” one particular value,and/or to “about” another particular value. By “about” is meant within5% of the value, e.g., within 4, 3, 2, or 1% of the value. When such arange is expressed, another aspect includes from the one particularvalue and/or to the other particular value. Similarly, when values areexpressed as approximations, by use of the antecedent “about,” it willbe understood that the particular value forms another aspect. It will befurther understood that the endpoints of each of the ranges aresignificant both in relation to the other endpoint, and independently ofthe other endpoint.

The term “inhibit” refers to a decrease in an activity, response,condition, disease, or other biological parameter. This can include butis not limited to the complete ablation of the activity, response,condition, or disease. This may also include, for example, a 10%reduction in the activity, response, condition, or disease as comparedto the native or control level. Thus, the reduction can be a 10, 20, 30,40, 50, 60, 70, 80, 90, 100%, or any amount of reduction in between ascompared to native or control levels.

The term “subject” refers to any individual who is the target ofadministration or treatment. The subject can be a vertebrate, forexample, a mammal. Thus, the subject can be a human or veterinarypatient. The term “patient” refers to a subject under the treatment of aclinician, e.g., physician.

By “reduce” or other forms of the word, such as “reducing” or“reduction,” is meant lowering of an event or characteristic (e.g.,tumor growth). It is understood that this is typically in relation tosome standard or expected value, in other words it is relative, but thatit is not always necessary for the standard or relative value to bereferred to. For example, “reduces tumor growth” means reducing the rateof growth of a tumor relative to a standard or a control.

By “prevent” or other forms of the word, such as “preventing” or“prevention,” is meant to stop a particular event or characteristic, tostabilize or delay the development or progression of a particular eventor characteristic, or to minimize the chances that a particular event orcharacteristic will occur. Prevent does not require comparison to acontrol as it is typically more absolute than, for example, reduce. Asused herein, something could be reduced but not prevented, but somethingthat is reduced could also be prevented. Likewise, something could beprevented but not reduced, but something that is prevented could also bereduced. It is understood that where reduce or prevent are used, unlessspecifically indicated otherwise, the use of the other word is alsoexpressly disclosed.

The term “treat,” or other forms of the word, such as “treated” or“treatment,” refers to the medical management of a patient with theintent to cure, ameliorate, stabilize, or prevent a disease,pathological condition, or disorder. This term includes activetreatment, that is, treatment directed specifically toward theimprovement of a disease, pathological condition, or disorder, and alsoincludes causal treatment, that is, treatment directed toward removal ofthe cause of the associated disease, pathological condition, ordisorder. In addition, this term includes palliative treatment, that is,treatment designed for the relief of symptoms rather than the curing ofthe disease, pathological condition, or disorder; preventativetreatment, that is, treatment directed to minimizing or partially orcompletely inhibiting the development of the associated disease,pathological condition, or disorder; and supportive treatment, that is,treatment employed to supplement another specific therapy directedtoward the improvement of the associated disease, pathologicalcondition, or disorder.

The term “anticancer” refers to the ability to treat or control cellularproliferation and/or tumor growth at any concentration.

The term “cell membrane motion” refers to any detectable movement of orwithin a cell’s membrane that ceases once the cell is dead.

It is understood that throughout this specification the identifiers“first” and “second” are used solely to aid in distinguishing thevarious components and steps of the disclosed subject matter. Theidentifiers “first” and “second” are not intended to imply anyparticular order, amount, preference, or importance to the components orsteps modified by these terms.

Reference will now be made in detail to specific aspects of thedisclosed materials, compounds, compositions, articles, and methods,examples of which are illustrated in the accompanying Examples andFigures.

Methods

Accurate preclinical predictions of the clinical efficacy ofexperimental cancer drugs are highly desired but often haphazard. Suchpredictions can be improved by incorporating elements of the tumormicroenvironment in preclinical models by providing a more physiologicalsetting. In generating improved xenograft models, the use of primarytumors from patients is preferable to clonal tumor cell lines.

Disclosed herein are systems and methods comprising a dose-responseplatform, for in vitro screening of drugs. Also disclosed herein aresystems and methods comprising a computational model of clinicalresponse. In some examples, the systems and methods can combine thedose-response platform, for in vitro screening of drugs and thecomputational model of clinical response. In some examples, the in vitrocomponent can include a 3D reconstruction of a cancer microenvironment,e.g., including primary cancer cells, extracellular matrix, andpatient-derived stroma and growth factors. In some examples, livemicroscopy and digital image analysis can be used to detect cell deathevents in different drug concentrations, which can then be used togenerate dose-response surfaces. In some examples, an evolutionarycomputational model designed to simulate how a heterogeneous populationof cancer cells responds to therapy is used as an in silico component ofthe methods described herein. From the in vitro data, the model canidentify the size and chemosensitivity of subpopulations within thepatient’s tumor burden, and simulate how the tumor would respond to thedrug(s) in physiological conditions in a clinical regimen.

Pre-clinical assays specifically designed to generate data toparameterize such computational models, preferably comply with one ormore of the following conditions: (a) compatibility with patient primarycancer cells; (b) recapitulate the tumor microenvironment, namelyextra-cellular matrix and stroma; (c) be non-destructive, solongitudinal studies can be performed, incorporating the temporaldimension; (d) use as few cells per experimental condition as possible,so each patient sample could be tested against a panel ofchemotherapeutic agents, in different environmental conditions; and (e)the data generated should result in testable clinical predictions, suchas the depth of response and/or progression-free survival (PFS).

Disclosed herein are non-destructive methods for quantifying cellviability. In some examples, the method can comprise culturing aplurality of cells from a subject in a chamber; capturing a firstoptical signal from the cells at a first time point; capturing a secondoptical signal from the cells at a second time point; analyzing thefirst optical signal and the second optical signal to detect cellmembrane motion of the cells; and analyzing the cell membrane motion toquantify the viability of the cells. In some embodiments, the method isused to quantify cell viability after the cells have been exposed to anactive agent. Therefore, in some embodiments, the method furthercomprises contacting the cells with an active agent and then quantifyingthe effect of the active agent on cell membrane motion (i.e.,viability).

In some examples, the cells can comprise cancer. Examples include cancerand/or tumors of the anus, bile duct, bladder, bone, bone marrow, bowel(including colon and rectum), breast, eye, gall bladder, kidney, mouth,larynx, esophagus, stomach, testis, cervix, head, neck, ovary, lung,mesothelioma, neuroendocrine, penis, skin, spinal cord, thyroid, vagina,vulva, uterus, liver, muscle, pancreas, prostate, blood cells (includinglymphocytes and other immune system cells), and brain. Other examples ofcancers include adrenocortical carcinoma, adrenocortical carcinoma,cerebellar astrocytoma, basal cell carcinoma, bile duct cancer, bladdercancer, bone cancer, brain tumor, breast cancer, Burkitt’s lymphoma,carcinoid tumor, central nervous system lymphoma, cervical cancer,chronic myeloproliferative disorders, colon cancer, cutaneous T-celllymphoma, endometrial cancer, ependymoma, esophageal cancer, gallbladdercancer, gastric (stomach) cancer, gastrointestinal carcinoid tumor, germcell tumor, glioma,, hairy cell leukemia, head and neck cancer,hepatocellular (liver) cancer, hypopharyngeal cancer, hypothalamic andvisual pathway glioma, intraocular melanoma, retinoblastoma, islet cellcarcinoma (endocrine pancreas), laryngeal cancer, lip and oral cavitycancer, liver cancer, medulloblastoma, Merkel cell carcinoma, squamousneck cancer with occult mycosis fungoides, myelodysplastic syndromes,myelogenous leukemia, nasal cavity and paranasal sinus cancer,nasopharyngeal cancer, neuroblastoma, non-small cell lungcancer, oralcancer, oropharyngeal cancer, osteosarcoma, ovarian cancer, pancreaticcancer, paranasal sinus and nasal cavity cancer, parathyroid cancer,penile cancer, pheochromocytoma, pineoblastoma and supratentorialprimitive neuroectodermal tumor, pituitary tumor, plasma cellneoplasm/multiple myeloma, pleuropulmonary blastoma, prostate cancer,rectal cancer, renal cell (kidney) cancer, retinoblastoma,rhabdomyosarcoma, salivary gland cancer, Ewing’s sarcoma, soft tissuesarcoma, Sezary syndrome, skin cancer, small cell lung cancer, smallintestine cancer, supratentorial primitive neuroectodermal tumors,testicular cancer, thymic carcinoma, thymoma, thyroid cancer,transitional cell cancer of the renal pelvis and ureter, trophoblastictumor, urethral cancer, uterine cancer, vaginal cancer, vulvar cancer,Waldenström’s macroglobulinemia, and Wilms’ tumor.

In some examples, the cancer can comprise a hematological cancer.Hematological cancers are the types of cancer that affect blood, bonemarrow and lymph nodes. As the three are intimately connected throughthe immune system, a disease affecting one of the three will oftenaffect the others as well. Hematological cancers may derive from eitherof the two major blood cell lineages: myeloid and lymphoid cell lines.The myeloid cell line normally produces granulocytes, erythrocytes,thrombocytes, macrophages and mast cells; the lymphoid cell lineproduces B, T, NK and plasma cells. Lymphomas, lymphocytic leukemias,and myeloma are from the lymphoid cell line, while acute and chronicmyelogenous leukemia, myelodysplastic syndromes and myeloproliferativediseases are myeloid in origin.

In some examples, the cancer can comprise multiple myeloma. Multiplemyeloma is the second most common hematological cancer in the UnitedStates, and constitutes 1% of all cancers. Specifically, multiplemyeloma is a cancer of plasma cells, a type of white blood cell normallyresponsible for producing antibodies. In multiple myeloma, collectionsof abnormal plasma cells accumulate in the bone marrow, where theyinterfere with the production of normal blood cells. Kidney problems,bone lesions and hypercalcemia are common complications associated withmultiple myeloma. Myeloma develops in 1-4 per 100,000 people per year.It is more common in men, and is twice as common in African-Americans asit is in European-Americans. With conventional treatment, mediansurvival is 3-4 years, which may be extended to 5-7 years or longer withadvanced treatments.

The chamber can comprise any chamber consistent with the methodsdescribed herein. Examples of suitable chambers can include, but are notlimited to, petri dishes, laboratory flasks (e.g., Erlenmeyer flasks,beakers, conical flasks, round bottom flasks, culture flasks),microfluidic chambers, multiwell-pates, and the like. In some examples,the chamber can comprise any chamber that allows for bright fieldimaging. In some examples, the chamber can comprise a microfluidicchamber. In some examples, the chamber can comprise a well in amultiwell-plate.

In some examples, the chamber can recapitulate the cancermicroenvironment. In some examples, the culturing a plurality of cancercells from a subject in a chamber can include a 3D reconstruction of thecancer microenvironment, e.g., including primary cancer cells,extracellular matrix, and patient-derived stroma and growth factors.

The active agent can comprise a wide variety of drugs, includingantagonists, for example enzyme inhibitors, and agonists, for example atranscription factor which results in an increase in the expression of adesirable gene product (although as will be appreciated by those in theart, antagonistic transcription factors can also be used), are allincluded. In addition, the active agent includes those agents capable ofdirect toxicity and/or capable of inducing toxicity towards healthyand/or unhealthy cells in the body. Also, the active agent can becapable of inducing and/or priming the immune system against potentialpathogens.

The active agent can, for example, comprise an anticancer agent,antiviral agent, antimicrobial agent, anti-inflammatory agent,immunosuppressive agent, anesthetics, or any combination thereof.

In some examples, the active agent can comprise an anticancer agent.Examples of anticancer agents include 13-cis-Retinoic Acid,2-Amino-6-Mercaptopurine, 2-CdA, 2-Chlorodeoxyadenosine, 5-fluorouracil,6-Thioguanine, 6-Mercaptopurine, Accutane, Actinomycin-D, Adriamycin,Adrucil, Agrylin, Ala-Cort, Aldesleukin, Alemtuzumab, Alitretinoin,Alkaban-AQ, Alkeran, All-transretinoic acid, Alpha interferon,Altretamine, Amethopterin, Amifostine, Aminoglutethimide, Anagrelide,Anandron, Anastrozole, Arabinosylcytosine, Aranesp, Aredia, Arimidex,Aromasin, Arsenic trioxide, Asparaginase, ATRA, Avastin, BCG, BCNU,Bevacizumab, Bexarotene, Bicalutamide, BiCNU, Blenoxane, Bleomycin,Bortezomib, Busulfan, Busulfex, C225, Calcium Leucovorin, Campath,Camptosar, Camptothecin-11, Capecitabine, Carac, Carboplatin,Carmustine, Carmustine wafer, Casodex, CCNU, CDDP, CeeNU, Cerubidine,cetuximab, Chlorambucil, Cisplatin, Citrovorum Factor, Cladribine,Cortisone, Cosmegen, CPT-11, Cyclophosphamide, Cytadren, Cytarabine,Cytarabine liposomal, Cytosar-U, Cytoxan, Dacarbazine, Dactinomycin,Darbepoetin alfa, Daunomycin, Daunorubicin, Daunorubicin hydrochloride,Daunorubicin liposomal, DaunoXome, Decadron, Delta-Cortef, Deltasone,Denileukin diftitox, DepoCyt, Dexamethasone, Dexamethasone acetate,Dexamethasone sodium phosphate, Dexasone, Dexrazoxane, DHAD, DIC,Diodex, Docetaxel, Doxil, Doxorubicin, Doxorubicin liposomal, Droxia,DTIC, DTIC-Dome, Duralone, Efudex, Eligard, Ellence, Eloxatin, Elspar,Emcyt, Epirubicin, Epoetin alfa, Erbitux, Erwinia L-asparaginase,Estramustine, Ethyol, Etopophos, Etoposide, Etoposide phosphate,Eulexin, Evista, Exemestane, Fareston, Faslodex, Femara, Filgrastim,Floxuridine, Fludara, Fludarabine, Fluoroplex, Fluorouracil,Fluorouracil (cream), Fluoxymesterone, Flutamide, Folinic Acid, FUDR,Fulvestrant, G-CSF, Gefitinib, Gemcitabine, Gemtuzumab ozogamicin,Gemzar, Gleevec, Lupron, Lupron Depot, Matulane, Maxidex,Mechlorethamine, -Mechlorethamine Hydrochlorine, Medralone, Medrol,Megace, Megestrol, Megestrol Acetate, Melphalan, Mercaptopurine, Mesna,Mesnex, Methotrexate, Methotrexate Sodium, Methylprednisolone, Mylocel,Letrozole, Neosar, Neulasta, Neumega, Neupogen, Nilandron, Nilutamide,Nitrogen Mustard, Novaldex, Novantrone, Octreotide, Octreotide acetate,Oncospar, Oncovin, Ontak, Onxal, Oprevelkin, Orapred, Orasone,Oxaliplatin, Paclitaxel, Pamidronate, Panretin, Paraplatin, Pediapred,PEG Interferon, Pegaspargase, Pegfilgrastim, PEG-INTRON,PEG-L-asparaginase, Phenylalanine Mustard, Platinol, Platinol-AQ,Prednisolone, Prednisone, Prelone, Procarbazine, PROCRIT, Proleukin,Prolifcprospan 20 with Carmustine implant, Purinethol, Raloxifene,Rheumatrex, Rituxan, Rituximab, Roveron-A (interferon alfa-2a), Rubex,Rubidomycin hydrochloride, Sandostatin, Sandostatin LAR, Sargramostim,Solu-Cortef, Solu-Medrol, STI-571, Streptozocin, Tamoxifen, Targretin,Taxol, Taxotere, Temodar, Temozolomide, Teniposide, TESPA, Thalidomide,Thalomid, TheraCys, Thioguanine, Thioguanine Tabloid, Thiophosphoamide,Thioplex, Thiotepa, TICE, Toposar, Topotecan, Toremifene, Trastuzumab,Tretinoin, Trexall, Trisenox, TSPA, VCR, Velban, Velcade, VePesid,Vesanoid, Viadur, Vinblastine, Vinblastine Sulfate, Vincasar Pfs,Vincristine, Vinorelbine, Vinorelbine tartrate, VLB, VP-16, Vumon,Xeloda, Zanosar, Zevalin, Zinecard, Zoladex, Zoledronic acid, Zometa,Gliadel wafer, Glivec, GM-CSF, Goserelin, granulocyte colony stimulatingfactor, Halotestin, Herceptin, Hexadrol, Hexalen, Hexamethylmelamine,HMM, Hycamtin, Hydrea, Hydrocort Acetate, Hydrocortisone, Hydrocortisonesodium phosphate, Hydrocortisone sodium succinate, Hydrocortonephosphate, Hydroxyurca, Ibritumomab, Ibritumomab Tiuxetan, Idamycin,Idarubiein, Ifex, IFN-alpha, Ifosfamide, IL 2, IL-11, Imatinib mesylate,Imidazole Carboxamide, Interferon alfa, Interferon Alfa-2b (PEGconjugate), Interleukin 2, Interleukin-11, Intron A (interferonalfa-2b), Leucovorin, Leukeran, Leukine, Leuprolide, Leurocristine,Leustatin, Liposomal Ara-C, Liquid Pred, Lomustine, L-PAM, L-Sarcolysin,Meticorten, Mitomycin, Mitomycin-C, Mitoxantrone, M-Prednisol, MTC, MTX,Mustargen, Mustine, Mutamycin, Myleran, Iressa, Irinotecan,Isotretinoin, Kidrolase, Lanacort, L-asparaginase, LCR, FAM-HYD-1,Marizomib (NPI-0052), Lenalidomide, Carfilzomib, Panobinostat,Quisinostat, Selinexor, and Oprozomib. The anticancer agent can alsoinclude biopharmaceuticals such as, for example, antibodies.

In some examples, the active agent can comprise a combination of activeagents.

In some examples, the active agent can comprise melphalan, bortezomib,FAM-HYD-1, Marizomib (NPI-0052), Carfilzomib, Cytoxan, Dexamethasone,Thalidomide, Lenalidomide, Oprozomib, Panobinostat, Quisinostat,Selinexor, or a combination thereof. Bortezomib, carfilzomib, andoprozomib are proteasome inhibitors, whereas melphalan is an alkylatingagent. They are approved for the treatment of multiple myeloma, as wellas other diseases. FAM-HYD-1 is a conjugate of the fluorescent moleculefluorescein (FAM) and the 1.5 kDa peptide HYD-1, an experimental drugwith direct toxicity to MM cells (Nair RR, Emmons MF, et al. Mol CancerTher 2009;8:2441-51). Panobinostat and Quisinostat are experimentalhistone deacetylase (HDAC) inhibitors in clinical trials for treatmentof multiple myeloma patients. Selinexor is a nuclear export inhibitoralso in clinical trials for treatment of multiple mycloma.

Contacting the cells with the active agent can be accomplished by anysuitable method and technique presently or prospectively known to thoseskilled in the art. Administration of the active agent can be a singleadministration, or at continuous or distinct intervals as can be readilydetermined by a person skilled in the art.

In some examples, the first optical signal, the second optical signal,or a combination thereof involves any optical microscopy illuminationtechniques suitable to detect cell membrane activity, such as a brightfield illumination, dark field illumination, and phase contrastillumination.

Cell membrane motion can comprise, for example, observable changes inthe size and/or morphology of the cell membrane (e.g., cell membranemotion does not comprise translational motion of the cell). In someexamples, the absence of cell membrane motion can indicate cell death.

In some examples, the cells of the method are obtained by collecting asample from the subject and then isolating the cells from the sample. Asan example, the sample can comprise a bone marrow aspirate where thecells are hematological cancer cells isolated from the aspirate, e.g.,by flow cytometry using a cell surface cancer marker.

In some examples, the method can further comprise collecting parametersfrom the viability observations to generate a multi-parameter model thatsummarizes the response of a cancer in a subject to the active agent.These parameters can include, for example, drug concentration, exposuretime, IC50, EC50, and drug free doubling time, as well as clinicalinformation from the patient, such as previous response to drugs andrate of tumor regrowth as measured by surrogate measurements such asblood or urine para-proteins. Computational methods, such as thosedisclosed herein, may be parameterized by data from the disclosed methodand used to estimate response to treatment with the drug being tested.

Also disclosed herein are methods for predicting a response of a subjectto treatment with an active agent. The methods can comprise firstpreparing a three-dimensional dose-response curve by assessing theviability of cells from the subject in response to the active agent at aplurality of time points at a plurality of dosages. The method can theninvolve generating a multi-parameter model that summarizes thethree-dimensional dose-response curve. The multi-parameter model canthen be used to calculate the rate of accumulation of damage in thecells due to the active agent and the active agent-induced cell deathdue to the accumulated damage. In some embodiments, the number ofdistinct populations (e.g., in terms of sensitivity to the active agent)in the cells is a covariate in the multi-parameter model, so the methodcan involve determining the number of populations. The rate ofaccumulation of damage in the cells and the active agent-induced celldeath due to the accumulated damage can then be extrapolated to predicta response of the subject to the active agent. For example, athree-dimensional dose-response curve based on 2, 3, 4, 5, 6, 7 days ofviability data can be extrapolated to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, ormore years of response by the subject.

In some examples, assessing the viability of the plurality of cells cancomprise any of the methods described above.

In some examples, the methods disclosed herein can further compriseselecting a cancer treatment regimen for the subject based on predictedresponses to 2, 3, 4, 5, 6, 7, 8, 9, 10, or more different activeagents.

In some examples, the method can predict an initial response of thesubject to the active agent. In some examples, the method can predictthe chance of progression-free survival. In some examples, the methodcan predict the chance of developing environment-mediated resistance tothe active agent. In some examples, the method can predict an effectivedosing schedule of the active agent. In some examples, the method canpredict an effective concentration of the active agent.

The methods disclosed herein can be carried out in whole or in part onone or more computing device. Therefore, also disclosed is a computersystem comprising memory on which is stored instructions to perform thedisclosed methods. Also disclosed herein are devices and modules withina device, wherein the device or module is configured to perform thedisclosed methods. For example, the memory can contain instructions toreceive optical signals from a device (e.g., imager), analyze the firstoptical signal and the second optical signal to detect cell membranemotion of the cells, and analyze the cell membrane motion to quantifythe viability of the cells following contact with the active agent. Insome examples, the memory can contain instructions to utilize adose-response curve to develop a multi-parameter model, wherein themulti-parameter model describes the rate of accumulation of damage inthe cells due to the active agent and the active agent-induced celldeath due to the accumulated damage; utilize the multi-parameter modeland the dose-response curve to determine the number of populations inthe sample; and utilize the number of populations and themulti-parameter model to predict a response of the subject to the activeagent.

FIG. 30 illustrates an example computing device upon which examplesdisclosed herein may be implemented. The computing device (160) caninclude a bus or other communication mechanism for communicatinginformation among various components of the computing device (160). Inits most basic configuration, computing device (160) typically includesat least one processing unit (212) (a processor) and system memory(214). Depending on the exact configuration and type of computingdevice, system memory (214) may be volatile (such as random accessmemory (RAM)), non-volatile (such as read-only memory (ROM), flashmemory, etc.), or some combination of the two. This most basicconfiguration is illustrated in FIG. 30 by a dashed line (210). Theprocessing unit (212) may be a standard programmable processor thatperforms arithmetic and logic operations necessary for operation of thecomputing device (160).

The computing device (160) can have additional features/functionality.For example, computing device (160) may include additional storage suchas removable storage (216) and non-removable storage (218) including,but not limited to, magnetic or optical disks or tapes. The computingdevice (160) can also contain network connection(s) (224) that allow thedevice to communicate with other devices. The computing device (160) canalso have input device(s) (222) such as a keyboard, mouse, touch screen,antenna or other systems. Output device(s) (220) such as a display,speakers, printer, etc. may also be included. The additional devices canbe connected to the bus in order to facilitate communication of dataamong the components of the computing device (160).

The processing unit (212) can be configured to execute program codeencoded in tangible, computer-readable media. Computer-readable mediarefers to any media that is capable of providing data that causes thecomputing device (160) (i.e., a machine) to operate in a particularfashion. Various computer-readable media can be utilized to provideinstructions to the processing unit (212) for execution. Common forms ofcomputer-readable media include, for example, magnetic media, opticalmedia, physical media, memory chips or cartridges, a carrier wave, orany other medium from which a computer can read. Examplecomputer-readable media can include, but is not limited to, volatilemedia, non-volatile media and transmission media. Volatile andnon-volatile media can be implemented in any method or technology forstorage of information such as computer readable instructions, datastructures, program modules or other data and common forms are discussedin detail below. Transmission media can include coaxial cables, copperwires and/or fiber optic cables, as well as acoustic or light waves,such as those generated during radio-wave and infra-red datacommunication. Example tangible, computer-readable recording mediainclude, but are not limited to, an integrated circuit (e.g.,field-programmable gate array or application-specific TC), a hard disk,an optical disk, a magneto-optical disk, a floppy disk, a magnetic tape,a holographic storage medium, a solid-state device, RAM, ROM,electrically erasable program read-only memory (EEPROM), flash memory orother memory technology, CD-ROM, digital versatile disks (DVD) or otheroptical storage, magnetic cassettes, magnetic tape, magnetic diskstorage or other magnetic storage devices.

In an example implementation, the processing unit (212) can executeprogram code stored in the system memory (214). For example, the bus cancarry data to the system memory (214), from which the processing unit(212) receives and executes instructions. The data received by thesystem memory (214) can optionally be stored on the removable storage(216) or the non-removable storage (218) before or after execution bythe processing unit (212).

The computing device (160) typically includes a variety ofcomputer-readable media. Computer-readable media can be any availablemedia that can be accessed by device (160) and includes both volatileand non-volatile media, removable and non-removable media. Computerstorage media include volatile and non-volatile, and removable andnon-removable media implemented in any method or technology for storageof information such as computer readable instructions, data structures,program modules or other data. System memory (214), removable storage(216), and non-removable storage (218) are all examples of computerstorage media. Computer storage media include, but are not limited to,RAM, ROM, electrically erasable program read-only memory (EEPROM), flashmemory or other memory technology, CD-ROM, digital versatile disks (DVD)or other optical storage, magnetic cassettes, magnetic tape, magneticdisk storage or other magnetic storage devices, or any other mediumwhich can be used to store the desired information and which can beaccessed by computing device (160). Any such computer storage media canbe part of computing device (160).

It should be understood that the various techniques described herein canbe implemented in connection with hardware or software or, whereappropriate, with a combination thereof. Thus, the methods, systems, andassociated signal processing of the presently disclosed subject matter,or certain aspects or portions thereof, can take the form of programcode (i.e., instructions) embodied in tangible media, such as floppydiskettes, CD-ROMs, hard drives, or any other machine-readable storagemedium wherein, when the program code is loaded into and executed by amachine, such as a computing device, the machine becomes an apparatusfor practicing the presently disclosed subject matter. In the case ofprogram code execution on programmable computers, the computing devicegenerally includes a processor, a storage medium readable by theprocessor (including volatile and non-volatile memory and/or storageelements), at least one input device, and at least one output device.One or more programs can implement or utilize the processes described inconnection with the presently disclosed subject matter, e.g., throughthe use of an application programming interface (API), reusablecontrols, or the like. Such programs can be implemented in a high levelprocedural or object-oriented programming language to communicate with acomputer system. However, the program(s) can be implemented in assemblyor machine language, if desired. In any case, the language can be acompiled or interpreted language and it may be combined with hardwareimplementations.

Also disclosed herein are methods for selecting a cancer treatmentregimen for a subject. The method can involve an in vitro microfluidicdose-response assay of a sample from a cancer of a subject to identifythe response to an anticancer agent, such as a chemotherapeutic agent,compared to a control. The assay can involve the use of an observationchamber for visualizing cancer cells from the sample during the method.In some embodiments, the chemotherapeutic agent is diffused from onereservoir of a microfluidic chamber to the other thereby creating astable gradient across the observation chamber. In some embodiments,cells are imaged continuously, allowing for the effect of time to beassessed.

In some examples, the method can further involve identifying cell deathinduced by the drug. Typical membrane-impermeable probes for detectionof cell death, such as EthD-1, present a significant variation in thetime for fluorescence acquisition after death in cell lines or patientsamples. To avoid this confounding effect, disclosed is an approach thatidentifies cell death based of motion of the membrane. In someembodiments, the identification of cell death comprises: (a) collectinga first bright field image of a cancer cell at a first time; (b)collecting a second bright field image of a cancer cell at a secondtime; (c) applying an algorithm to the first and second images toidentify the presence or absence of cell membrane motion; wherein theabsence of cell membrane motion indicates cell death. Typical cellviability assays are often destructive or cytotoxic, if carried for longperiods of time, limiting the information acquired in the temporaldimension. In the disclosed system and method, cancer cells, stroma andmatrix do not have to be separated, and no cytotoxic agents have to beused to determine cell viability, thus allowing longitudinal studies ofdrug activity without interfering with the microenvironment. In someembodiments, only bright field imaging is used, thereby eliminating anytoxicity from viability markers.

In some embodiments, the in vitro microfluidic dose-response assaycomprises a combination of primary cancer cells from the sample,extracellular matrix, subject-derived stroma, and one or more growthfactors. The extracellular matrix and stroma are components ofchemoresistance in many tumors. However, the inclusion of these elementssignificantly increases the complexity of dose response assays, oftenrequiring the separation between cancer and stromal cells, by matrixdigestion and/or flow sorting (Misund K, Baranowska KA, et al. J BiomolScreen 2013;18:637-46). Cell adhesion mediated drug resistance (CAMDR)is believed to be a cause of minimal residual disease in multiplemyeloma (Meads MB, Gatenby RA, Dalton WS. Nat Rev Cancer 2009;9:665-74).In some embodiments, the assay allows for assessment ofenvironment-mediated drug resistance.

In cancers such as MM, where a few million cells are obtainable perpatient biopsy, it is important to minimize the number of cells perexperimental condition. In some embodiments, less than 20,000 cancercells are used in the assay described herein (for example, less than20,000; 15,000; 10,000; 5,000 or 2,000 cells). In some embodiments, morethan 1,000 cells are used in the assay (for example, at least 1,000;2,000; 3,000; 4,000; 5,000; 6,000, 7,000; 8,000; 9,000; or 10,000cells). In some embodiments, 1,000 - 10,000 cells are used in the assay(for example, at least 1,000; 2,000; 3,000; 4,000; 5,000; 6,000, 7,000;8,000; 9,000 or 10,000 cells).

The disclosed system and method can further involve collectingparameters from the assay to generate a multi-parameter model thatsummarized the response of the subject to the drug treatment. Theseparameters include, for example, drug concentration, exposure time,IC50, EC50, and drug free doubling time. Computational methods, such asthose disclosed herein, may be parameterized by data from the disclosedmethod and used to estimate response to treatment with the drug beingtested.

The disclosed system and method can be used to select a cancer treatmentregimen for the subject based on the results of the multi-parametermodel. In some embodiments, the integration between in vitro and insilico computational models allows for assessment of initial response toa drug. In some embodiments, the integration between in vitro andcomputational models allows for assessment of the progression-freesurvival.

In some embodiments, the cancer is a hematological malignancy. In someembodiments, the sample is a bone marrow aspiration. In someembodiments, the cancer is multiple myeloma.

The disclosed method may be used to identify drug candidates for anycancer type or subtype. A representative but non-limiting list ofcancers include lymphoma, B cell lymphoma, T cell lymphoma, mycosisfungoides, Hodgkin’s Disease, myeloid leukemia, bladder cancer, braincancer, nervous system cancer, head and neck cancer, squamous cellcarcinoma of head and neck, kidney cancer, lung cancers such as smallcell lung cancer and non-small cell lung cancer,neuroblastoma/glioblastoma, ovarian cancer, pancreatic cancer, prostatecancer, skin cancer, liver cancer, melanoma, squamous cell carcinomas ofthe mouth, throat, larynx, and lung, colon cancer, cervical cancer,cervical carcinoma, breast cancer, epithelial cancer, renal cancer,genitourinary cancer, pulmonary cancer, esophageal carcinoma, head andneck carcinoma, large bowel cancer, hematopoietic cancers (e.g.,leukemia); testicular cancer; rectal cancers, prostatic cancer, andpancreatic cancer.

In some embodiments, combinations of drugs are tested. In some cases,the dosing schedule of a combination of drugs is tested. In someembodiments, the heterogeneity of drug response is assessed. In someembodiments, the drug comprises melphalan, bortezomib, FAM-HYD-1 orcombinations thereof.

EXAMPLES Example 1 Materials and Methods

Cell lines. The human myeloma cell lines used were RPMI-8226,HS-5/GFP-labeled, NCI-H929 and 8226/LR-5. The 8226/dsRed2 cell line wasstably transfected with the fluorescent protein dsRed2. All cells weremaintained in culture with RPMI 1640 (Gibco) media supplemented with 10%heat inactivated fetal bovine serum (Life Technologies) and 1%penicillin-streptomycin solution (Invitrogen), in incubators at 5% CO₂,37° C. Melphalan-resistant 8226/LR-5 cells were maintained in 5 µMmelphalan in medium, and cultured in drug-free medium for 2 weeks priorto experiments.

Primary cancer cells. The in vitro response of cancer cells from 7 MMpatients were investigated. The medical records were de-identified andonly the following clinical-relevant information was reviewed: (A)treatment administered (chemotherapeutic agents, doses and schedule)prior to biopsy; (B) cytogenetics; (C) blood and urine electrophoresisresults. Patients received standard-of care treatment, and consented toprovide an extra sample of bone marrow aspirate during a routine biopsy.These aspirates were used in the in vitro assays further described.After informed written consent, bone marrow aspirates were obtained frommultiple myeloma patients either newly diagnosed or with refractorydisease. Processing of bone marrow aspirate and selection of MM cells isdescribed below. MM cells were seeded into the Tbidi µ-slide Chemotaxis3D device under experimental culture conditions (described below) within4 hours of each patient biopsy.

Processing of bone marrow aspirates. Clinical bone marrow aspirates (20mL) from patients were collected in sodium heparin syringe, andmononuclear cells were immediately isolated by centrifuging dilutedmarrow (1:1 with sterile PBS) over a Ficoll-Paque Plus (AmershamBiosciences) gradient at 400 x g for 30 minutes at ambient temperature.The interface was removed, cells washed with cold PBS and counted. Onecytospin slide was prepared and stained with Wright-Giemsa stain toassess plasma cell percentage. The amount of CD138 beads (Miltenyi cat #130-051-301) used were according to number of cells and plasma cellpercentage. If starting sample was less than 20% plasma cells, the cellswere resuspended using 90 µl separation buffer and 10 µl CD138 beadswere added per 5×10⁶ cells. If starting sample is more than 20% plasmacells, the cells were resuspended using 80 µl separation buffer and 20µl CD138 beads per 1×10⁷ cells. After a 15 minute incubation with beadsat 4° C., the cells were passed through a 35 µm strainer added topre-wetted LS columns (Miltenyi cat # 130-042-401) placed in a magneticfield (Miltenyi MidiMACS magnet). The column was washed 3 times andcollected before removing from magnet and eluting CD138 enriched cellswith 1 ml of separation buffer. CD 138 enrichment was assessed withanother stained cytospin slide. Serum from each patient was filteredwith a .22 micron syringe filter and was used to make supplementedRPMI1640 growth media with 10% heat inactivated fetal bovine serum, 10%patient serum, 1% penicillin-streptomycin.

Drugs. The following chemotherapeutic agents were tested: bortezomib(Selleckchem), melphalan (Sigma), and FAM-HYD-1.

In vitro dose response assays in 3D microfluidic chambers. Commerciallyavailable 3D cell culture slides (µ-slide Chemotaxis 3D Ibitreat fromIbidi, LLC) were gas and temperature equilibrated at 37° C., 5% CO₂overnight prior to cell seeding. Each slide is comprised of threeseparate chambers each with a 1 mm wide, 50 µm high cell-viewing chamberthat holds a volume of 6 µL. It is connected to two 65 µL reservoirsalong both sides. Linear chemical gradients form across the cell chambervia passive diffusion. Aliquots consisting of 6.67 µL 10x MEM (LifeTechnologies), 6.67 µL deionized H₂O, 3.33 µL 7.5% sodium bicarbonatesolution (Life Technologies), and 16.67µL 1x RPMT 1640 (LifeTechnologies), were premixed and stored at 4° C. prior to experiments,as per manufacturer (Ibidi) instructions. 50 µL of 3.1 mg/mL Bovinecollagen type I (Advanced BioMatrix) was added at time of seeding. 16.67µL of cells suspended in RPMI 1640 were mixed into the collagen/mediamix to a final volume of 100 µL in 1.5 mg/mL bovine collagen 1 (6-folddilution of RPMI 1640 cell suspension). 6 µL of this cell/matrix mixwere used to load each viewing chamber. For cell lines in single cultureor mixed culture, the final concentration of cells was 3×10⁶ myelomacells/mL. For patient primary cells, the densities were 7×10⁶ cells/mLfor MM (CD138+), and 1×10⁶ cells/mL for mesenchymal cells. These celldensities were optimized to better reflect physiological cell density,and maximize the number of cells in the observation chamber, while stillmaintaining enough separation to allow the individual identification ofcells. Cell lines were seeded at lower density to account for theirlarger size and faster replication. The interval between mixing collagenwith cells and media, and seeding the chambers was kept below fiveminutes at ambient temperature to minimize collagen polymerization.After seeding, an additional 15 minutes at room temperature allowedadherent cells (HS-5 or patient stroma) to sink to the bottom of the 3Dchamber and keep the same focal plane for subsequent live imaging.Slides were then incubated at 37° C., 5% CO₂ for 1 hour. Collagenpolymerization was checked by visual inspection of fiber formation on aninverted phase contrast microscope with a 20X objective lens. Aftergelation, reservoirs on each side of the slide were filled with 65 µLculture media. 16.25 µL of 4x drug in culture media was dropped onto afilling port on the left reservoir and then an equal volume wasimmediately drawn out of the other filling port. Slides were then placedinto incubator for live imaging. For each experiment, there was acontrol with no drug added, which was used to detect spontaneous celldeath. For single culture experiments, chemotherapy was added 2-4 hafter cell seeding. For co-culture experiments with adherent stroma(HS-5 or patient stroma), drugs were added 24h later to ensure stromaadhesion.

Continuous versus pulsed exposure. In experiments with continuousexposure, the drug was maintained in media for the duration of theexperiment. If this duration exceeded 48h, the media on both reservoirswas completely removed, and replaced by fresh media, to which drug wasadded as previously described (16.25 µL at 4X concentration). In pulsedexposure experiments, the media on both reservoirs was completelyremoved, and replaced by fresh media at the end of the pulsed exposure.

Image acquisition. Two different models of fluorescence microscopes wereused for the experiments described herein: the first, JULT (DigitalBio), is a portable fluorescence microscope with bright field and redfluorescence capacities (ex/cm 630 nm/660 nm), which was maintainedinside a standard incubator for the duration of the experiments. Thesecond platform was the EVOS FL (AMG), a bench top fluorescencemicroscope (red channel ex/em 531 nm/593 nm), which used a stage-topheating stage/incubator (Tbidi), which maintained the cells at 37° C.,5% CO₂, and 80% humidity. For the experiments here described, imageswere acquired every 5-minute intervals. In experiments where the redfluorescent 8226/dsRed2 cell line was tested, or the cell-deathmolecular probe ethidium homodimer-1 (EthD-1) was used, both brightfield and red fluorescent channels were imaged, the first for changes incell morphology and membrane motion, and the second for loss of innatefluorescence or activity of EthD-1, respectively.

Quantification of drug concentration over time within microfluidicdevice. In order to quantify the shape and stability of the druggradient in the microfluidic device, a fluorophore-conjugated of thepeptide HYD-1 (1.5 kDa) was used within the dose-response assay, a 3Dgel matrix consisting of 1.5 mg/ml bovine collagen 1 with RPM11640/MEMmedia was placed into the culture chamber of the Ibidi microfluidicsdevice. After 45 minutes incubation at 37° C., reservoirs were filledwith RPMI1640 media 10% heat inactivated FBS, 1%penicillin-streptomycin. FAM-HYD1 was diluted into media beforereplacing ¼th of the volume in the left reservoir with fluorescent drugsolution (⅒ of stock). Fluorescence within the culture chamber wasimaged in an EVOS FL microscope using the GFP filter (ex/em 470 nm/525nm, 5X objective) with heated stage and gas incubation (37° C., 5% CO₂).Images were acquired at 1-minute intervals for 24 hours.

Digital image analysis. With a stable drug gradient established acrossthe main channel of the microfluidic slide, the observation channel wasdivided into five sections, or regions of interest (ROI), each with anaverage drug concentration of 100%, 80%, 60%, 40% and 20% of theconcentration in the drug reservoir, respectively. Sectioning thechannel into five areas was a compromise between a minimum number ofcells in each area, and the rounding due to the averaging of the drugconcentrations across each section. Dose response was quantified with amacro developed for the software ImageJ, further described. As discussedbelow, membrane-impermeable probes for detection of cell death, such asEthD-1, present a significant variation in the time for fluorescenceacquisition after death in cell lines or patient samples. To avoid thisconfounding effect, an approach that identifies cell death based ofmotion of the membrane was developed, described below.

Assessment of cell viability through membrane motion detection. It wasobserved that, although it was not possible to clearly discern a deadfrom a live cell based on the morphology in the bright field of a singleimage, all live cells suspended within the collagen matrix hadobservable membrane motion or shape changes, between two images taken ina 5-minute interval. These morphological changes abruptly stopped priorto cell death, indicating that this feature could be exploited as amarker for cell death. A macro for the open source software ImageJ wascreated using the plugins TurboReg (Thevenaz P, Ruttimann UE, Unser M.IEEE Trans Image Process 1998;7:27-41) and RunningZProjector. The macroquantifies the amount of cell membrane motion in the different regionsof interest, and writes a file with this information for each frame, ortime point. Briefly, the macro loads the stack of bright field imagestaken at 5-minute intervals, and aligns them using the plugin TurboReg.This action removes translational motion, such as sliding of themicrofluidic chamber, as well as vibration. Next, the native ImageJ“background subtraction” function was used with parameters “rolling ballradius=1 pixel” and “sliding parabolic” (Sternberg SR. Biomedical ImageProcessing. Computer 1983; 16:22-34). Background subtraction served tonormalize image sequences across different experiments and/ormicroscopes used to image the chambers, making cells appear as brightspots against a uniform dark background. Motion and small variations incell membranes were detected using the plugin RunningZProjector. Itdetects the maximum pixel intensity across a 6-frame/slice interval,corresponding to 30 minutes. The original image was then subtracted fromthe maximum pixel intensity projection, resulting in an image whereactively moving membranes appear as bright rings. ImageJ’s “Gaussianblur” filter was used to convert these bright rings into spots thatcover the entire cell, and produce overlaid images.

Validation of motion detection algorithm through fluorescence. Differentfluorescent-labeling agents for cell viability were tested aslive-imaging approaches for response to chemotherapy. However,cytotoxicity, photo bleaching, intercellular variability of delaybetween cell death and signal detection, and incomplete representationof viable/apoptotic/necrotic cell states added noise to the assay. Amultiple myeloma cell line was stably transfected with dsRed2(8226/dsRed2), and used as a reference to visually detect the cytotoxiceffect of drugs through loss of red fluorescence. RFP expression is anintrinsic marker for these cells: live cells will quickly losefluorescence upon cell death due to membrane burst accompanied byrelease of cytoplasmic components, including the fluorescent protein.

Validation of motion detection algorithm through bioluminescence.NCI-H929 cells were seeded in 96-well plates in culture media or in a 3Dcollagen matrix with culture media added on top of the cell/collagenlayer. In wells without collagen, 1.5×10⁵ cells were resuspended in 50µL of media for a final density of 3×10⁶ cells/mL. To more closelyresemble microfluidic assay conditions, 1.5×10⁵ cells were suspended in30 µL of 1.5 mg/mL collagen matrix and were left to polymerize at 37° C.for 1 hour. 20 µL of media was then added as a separate phase on top ofthe cell/collagen layer. Melphalan was serially diluted in 2-fold stepsto a final concentration range of 100 µM to 1.56 µM in 7 rows. The sameprocedure was performed for bortezomib to final concentrations of 20 nMto 0.31 nM. All conditions and controls were performed in triplicate.After 24 hours of continuous drug exposure at 37° C. and 5% CO₂, 50 µLCellTiterGlo was added to each well and the plates were placed on anorbital shaker at room temperature for 10 minutes. 20 minutes later,bioluminescence was measured at ambient temperature on a microplatereader. Percent cell viability was defined as luminescence normalized tocontrols at 24 hours.

Analysis of Experimental Data

The quantification of the dose response of the cells in the experimentused Matlab’s (MathWorks) function lsqeurveƒit, which finds thecoefficients that minimize the distance between a function and a set ofdata points.

The default function of dose response was written as Equation 1, and thedata points were the normalized viability in each region of interest(ROT) at a given time point and drug concentration:

$\begin{matrix}{Viability(\%) = 100 \times \frac{2^{\frac{\text{Δ}T}{T}}}{\left( {1 + \left( \frac{Rx}{IC_{50_{Rx}}} \right)^{expRx} \times \left( \frac{\text{Δ}T}{IC_{50_{\text{Δ}T}}} \right)^{expT}} \right)}} & \text{­­­(Equation 1)}\end{matrix}$

The goodness of the fit was calculated from a linear regression of thepoints of the fit equation with the actual observed experimental pointsusing Prism 5 (GraphPad) and quantifying the slope and R² of theregression. For each example, two hypotheses were tested: either thesample was composed of one or two sub-populations. When no significantdifferences were observed in R², the simplest model was used (onepopulation).

Equation 1 is the simplest expression that describes how a homogenouspopulation of MM cells responds to chemotherapy as a function ofconcentration and exposure time. A growth term was included in thenumerator of Equation 1, where T is the doubling time, and ΔT is thevariable representing drug exposure time. Rx represents the drugconcentration to which cells are exposed, while IC50_(Rx), IC50_(ΔT),expRx, and expT are constants that determine the drug concentration andexposure time that causes death of 50% of the MM cells, and thesteepness of the slope of the viability curve, respectively.

The alkylating agent melphalan has a short half-life in media and invivo of approximately 2 h, mainly due to hydrolysis (Samuels BL, BitranJD. J Clin Oncol 1995; 13:1786-99). It was observed, however, that inlong-term experiments, cells continue to die a week after melphalanexposure (see Results). For this class of drugs, a mathematicalexpression that encompasses drug half-life, DNA-damage, andDNA-damage-induced cell death was created (Equation 2).

$\begin{matrix}\begin{array}{l}{Viab(\%) = 100 \times Death \times Growth} \\{Death = \frac{1}{1 + \frac{CumulDamage^{\exp_{IC50}}}{IC_{50}}}} \\{CumulDamage\left( {t + dt} \right) = CumulDamage(t) + \left( {\int{Rx\, dt}} \right)^{\exp_{DMG}}} \\{Growth(t) = 2^{\frac{t}{\text{T} \times {({1 + CumulDamage{(t)} \times K_{\text{T}}})}}}} \\{Rx(t) = Rx_{0} \times 2^{\frac{t}{\text{T}_{Mel}}}}\end{array} & \text{­­­(Equation 2)}\end{matrix}$

“Death” and “Growth” are the two functions that determine the changes innumber of viable cells in a given drug concentration, at a certain timepoint. “Death” represents the probability that any given cell from apopulation will die as a function of accumulated DNA damage(“CumulDamage”), which in turn is proportional to the area under thecurve (AUC) of drug concentration “Rx” and exposure time “dt”. “expDMG”is an empirical exponent. “Growth” quantifies cell replication, whichdepends on the drug-free doubling time T, the amount of DNA damage“CumulDamage”, and an empirical proportional constant KT. In otherwords, DNA damage slows replication (Gardner SN. Cancer Res2000;60:1417-25). The last expression means that the concentration ofactive melphalan in media, Rx, decays with a half-life TMel of 2 h.

Equation 2 is an empirical expression, with the goal of interpolatingthe data points across time and concentration dimensions, whilerecapitulating known mechanisms of melphalan toxicity and degradation.It is not, however, the only possible expression possible, and it maynot properly compute the viability in concentrations or exposure timessignificantly higher than the experimental conditions.

Computational modeling of therapy. As a proof of principle, to exemplifythe application of these in vitro chemosensitivity assays in estimatingpatient response to therapy, a computational model (Silva AS, Kam Y, etal. Cancer Res 2012) was used to simulate a hypothetical single-agentbortezomib regimen in an animal model (s.c. NCI-H929 in SCID mouse), andfor four patients whose MM cells’ sensitivity to bortezomib were testedin vitro.

In this computational model, one or more sub-populations arerepresented, each with a size, a doubling time, and a level ofsensitivity to the chemotherapeutic agent tested. Carrying capacity,which is the maximum theoretical growth rate of the entire tumor burden,was estimated from the labeling index commonly observed in MM patients(~1-3%). Intra-tumoral competition was modeled by an equation thatdetermines that bigger populations have higher chance of replicatingthan smaller ones (Equation 3), a dynamic similar to genetic drift.

$\begin{matrix}\begin{array}{l}{N_{i}\left( {t + dt} \right) = N_{i}(t) \times \left( {1 + \left( \frac{Rx}{IC50_{Rxi}} \right)^{\exp RXi} \times \left( \frac{dt}{IC50_{\text{Δ}Ti}} \right)^{\exp Ti}} \right)^{- 1} \times} \\\left\{ {\left\lbrack {\left( {1 + LI} \right)^{\frac{dt}{\text{T}i}} - 1} \right\rbrack \times \frac{N_{i}(t)}{\sum{N_{j}(t)}} + 1} \right\}\end{array} & \text{­­­(Equation 3)}\end{matrix}$

Equation 3 describes how the size of a sub-population within the tumorburden (N_(i)) changes within an interval of time (dt) in response ofdrug-induced cell death induced by exposure to a drug at theconcentration Rx for the interval of time dt. The surviving cells mayreplicate at a rate determined by their labeling index (LI), theduration of their cell cycle (T), and the percentage that thesub-population represents in the total tumor burden.

Bortezomib concentration in blood is characterized by a peak of ~100 nM,followed by a sharp decrease, and a stable concentration of ~1-3 nMbetween 2 and 192 h post IV administration (1.3 mg/m2) (Ogawa Y, TobinaiK, et al. Cancer Sci 2008;99:140-4; Reece DE, Sullivan D, et al.Chemother Pharmacol 2011;67:57-67). The in vitro chemosensitivity datafrom patients 8, 11, 12, and 13 parameterized the computational modelsof clinical response for each of these patients in a hypotheticalsingle-agent bortezomib regimen, in which the bone marrow concentrationwould remain constant at 3 nM.

As a preliminary validation of the correlation between in vitro and invivo chemosensitivity, computational models parameterized by assays withthe human MM cell line NCI-H929 were used to estimate the response tobortezomib treatment of a sub-cutaneous mouse model, treated with 1mg/kg bortezomib biweekly (Ishii T, Seike T, et al. Blood Cancer J2012;2:e68). Pharmacokinetic studies have shown that such IV injectionsin mice cause a peak blood concentration of ~0.5 nM, and ~0.4 nM at 48h. For these simulations, a stable 0.4 nM concentration of bortezomib inthe bone marrow of these mice along the treatment was considered.NCI-H929 cells have a cell cycle of approximately 24 h, and in thesubcutaneous model the tumors have a doubling time of approximately 3.5days, indicating that in this animal model, approximately 20% of H929cells are actively replicating at a given time, which was used aslabeling index in the simulations.

Results

Characterization of shape and duration of drug gradient. The first stepof validating the in vitro platform was to determine the stability, andalso the duration of any transients during the formation of the druggradient across the observation chamber. For this purpose, a conjugateof the fluorescent molecule fluorescein (FAM) and the 1.5 kDa peptideHYD-1, an experimental drug with direct toxicity to MM cells (Nair RR,Emmons MF, et al. Mol Cancer Ther 2009;8:2441-51), was used. Liveimaging was used to quantify the fluorescence in images taken at1-minute intervals during 18 h (FIG. 1 ). The fluorescent signalgradient was stable for the interval of the experiment, and thetransient time for its formation was shorter than the period betweendrug injection in the slide and start of imaging (~5-10′).

Loss of membrane motion is a reliable maker of cell death. An algorithmfor detection of cell membrane motion was used to detect cell death inpatient primary cells, due to the significant variation of the delaybetween cell death and membrane permeabilization, and acquisition offluorescence from molecular probes. FIG. 2 depicts the delay between thedetection of cell death using the motion-detection algorithm, and lossof fluorescence in the stably transfected cell line 8226/dsRed2. FIG. 3exemplifies the delay of acquisition of the molecular probe Ethidiumhomodimer-1 (EthD-1) red fluorescence in NCI-H929 cells.

Effect of the proteasome inhibitor bortezomib. The cell line NCI-H929was exposed to a stable gradient of bortezomib (maximum concentration 10nM) for 24 h, and a dose-response surface was created (FIG. 4A).According to these results, the bortezomib concentration that would leadto a 50% reduction in the number of live cells after 24 h, compared tothe initial time point, was approximately 2.5 nM. The concentration thatwould lead to a 50% reduction in the number of live cells, compared tothe control at 24 h was approximately 1.9 nM. The same cell line wasseeded in a 96-well plate, in suspension or in collagen, and cellviability was measured using the ATP-based assay CellTiter-Glo (FIG.4C). The Pearson test produced “r” values of 0.8905 and 0.8704 (P values0.003 and 0.0049) for the correlation between the model and suspension,and collagen results, respectively.

Quantification of melphalan innate resistance in cell lines in singleculture. The melphalan sensitive and resistant cell lines NCI-H929 and8226/LR5 were exposed to stable gradients of melphalan for 24 h (highestconcentrations of 50 µM and 100 µM, respectively) and chemosensitivitywas quantified. The analysis of 8226/LR5 detected a sub-population ofsensitive cells (approximately 30%, FIG. 5A), indicating that this cellline is actually heterogeneous, a possible explanation for the loss ofresistance commonly observed when these cells are maintained inmelphalan-free medium for many weeks (Bellamy WT, Dalton WS, et al.Cancer Res 1991;51:995-1002). Melphalan concentration that induced 50%of death in cells (EC₅₀) for 24 h continuous exposure was approximately50 µM for 8226/LR5, and approximately 12 µM for H929. Long-term exposureto lower, more physiological doses (10-20 µM) of melphalan, however,indicated that, although all melphalan had been hydrolyzed in the first24 h in media, cell death continued to occur after 6 days of drugexposure (FIG. 6 ).

Quantification environment-mediated melphalan resistance. Cell adhesionmediated drug resistance (CAMDR) is believed to be a cause of minimalresidual disease in multiple myeloma (Meads MB, Gatenby RA, Dalton WS.Nat Rev Cancer 2009;9:665-74). This mechanism is caused by directMM-stroma cell adhesion, by paracrine loops of soluble factor secretion,or MM-extracellular matrix adhesion. In order to quantify the importanceof MM-stroma adhesion under physiological conditions (high density, inpresence of ECM), the MM cell line NCI-H929 was co-cultured with thebone marrow derived stromal cell line HS-5/GFP. A significant shifttowards resistance was observed at later time points (approximately24h), and was most expressive around the concentration of 20-30 µM (FIG.7 ).

Continuous versus pulsed exposure to drugs. To exemplify the study ofcontinuous versus pulsed exposure to drugs, two chambers with NCI-H929cells were exposed to bortezomib for 24 h. In one the medium wasreplaced by drug-free medium, while in the other fresh medium withbortezomib was added. Being a reversible proteasome inhibitor, theresults suggest that bortezomib-induced death stops upon drug withdrawal(FIG. 8 ), unlike melphalan (FIG. 6 ).

Melphalan chemosensitivity of primary MM cells in single and co-culture.From the 17 patient samples obtained so far in this protocol, the first10 were used for development and optimization of the platform. Theresults of the 7 others are here described. CD138+ sorted primary MMcells from patient 14, a newly diagnosed patient, were exposed for 48hto a stable gradient of 25 µM melphalan in single and co-culture, withpatient-derived stroma. As shown in FIG. 9 , adhesion to stromasignificantly increased the survival of MM cells, shifting the 48h EC₅₀from 2 µM in single culture to 12 µM in co-culture. This effect could becircumvented by combination of a proteasome inhibitor at sub-lethallevels (Yanamandra N, Colaco NM, et al. Clin Cancer Res 2006;12:591-9)(FIG. 10 ).

Melphalan and bortezomib chemosensitivity among MM patients. FIG. 11depicts the in vitro chemosensitivity of three MM patients to melphalanin single culture: patient 14, patient 11 (smoldering myeloma), andpatient 12 (relapsed after bone marrow transplantation). The EC₅₀s at 24h exposure were 4 µM for patients 14 and 12, and 1 µM for patient 11.However, the percentage surviving cells at 20 µM, a more physiologicalconcentration of high-dose melphalan treatment, was 30% for patient 12,11% for patient 14, and 4% for patient 11. FIG. 12 represents bortezomibchemosensitivity of patients 11, 12, 13 (newly diagnosed) and 17(smoldering myeloma). For patients 11 and 12, EC₅₀ after 24 h continuousexposure was below 2 nM, however, at higher concentrations, MM cellsfrom patient 11 were significantly more resistant: 30% live cells at 50nM bortezomib for patient 11, and ~8% for patient 12. 24 h EC₅₀ forpatient 13 was approximately 10 nM, while EC₅₀ was not reached with thesample from patient 17.

Extrapolation of in vitro data into in vivo and clinical response. Byparameterizing Equation 3 with values obtained from fitting Equation 1to the in vitro dose response data, it is possible to simulate how atumor mass would respond to a therapeutic regimen. As an example, thesub-cutaneous mouse model SCID (severe combined immunodeficient), whenimplanted with the cell line NCI-H929, develops a tumor that grows45-fold in 20 days (Nakashima T, Ishii T, et al. Clinical CancerResearch 2010;16:2792-802). When treated with 1 mg/kg bortezomib twice aweek, the tumor growth is reduced, and tumors are 20-fold bigger at day20 than at implantation (Ishii T, Seike T, et al. Blood Cancer J2012;2). From the bortezomib in vitro chemosensitivity assay with thecell line NCI-H929 (FIG. 4 ), the parameters from Equation 3 were:IC50Rx=10.35 nM, IC50ΔT=10.38 h, expRX=2.7, and expT=7.1. FIG. 13depicts the computational simulation of the tumor growth under controlconditions, under a bi-weekly treatment with 1 mg/kg of bortezomib(which leads to a stable blood concentration of 0.4 nM (Williamson MJ,Silva MD, et al. Mol Cancer Ther 2009;8:3234-43)), and a hypotheticalregimen where mice received a pulsed therapy with the same AUC (areaunder the curve), with bi-weekly injections of bortezomib every otherweek (therapy holidays). The simulated tumor would have increased53.4-fold in control conditions (Pearson r=0.9762), 18-fold in standardbortezomib treatment (Pearson r=0.9869), and 5-fold in the hypotheticalpulsed regimen. The same approach was used to simulate the response ofpatients 11, 12, 13, and 17 to a single agent regimen of bortezomib (1.3mg/m², FIG. 14 ). In this regimen, plasma concentration stabilizes atapproximately 1 nM (Reece DE, Sullivan D, et al. Chemother Pharmacol2011;67:57-67), and according to simulations, would achieve completeresponse in patients 11 an 12, relapse in patient 17, and no response inpatient 13.

Discussion:

An interdisciplinary platform to study pre-clinical drug activity inprimary MM cells has been described herein. First, MM cells wereembedded in a microfluidic chamber that recapitulates the bone marrowmicroenvironment, including high cell density, extracellular matrix andpatient-derived stromal cells. A linear and stable drug gradient wasestablished across the chamber, which is then imaged sequentially inbright field. A digital image analysis algorithm detected live MM cellsby the motion of cell membrane: upon death this activity ceases. Themeasurements of viability, at different concentrations and time points,were fit to mathematical models of chemosensitivity. These models canrepresent one or multiple sub-populations, and can be empirical ormechanistic. The data from these experiments can thus be used toparameterize mathematical models to simulate clinical outcome.

This platform overcomes some limitations of pre-clinical assays usingprimary cancer cells. It has been shown that extracellular matrix andstroma may be components of chemoresistance in many tumors. However, theinclusion of these elements significantly increases the complexity ofdose response assays, often requiring the separation between cancer andstromal cells, by matrix digestion and/or flow sorting (Misund K,Baranowska KA, et al. J Biomol Screen 2013;18:637-46). Also, viabilityassays are often destructive or cytotoxic, if carried for long periodsof time, limiting the information acquired in the temporal dimension. Inthe disclosed assay, MM cells, stroma and matrix were never separated,and no cytotoxic agents were used to determine cell viability, thusallowing longitudinal studies of drug activity without interfering withthe microenvironment.

In cancers such as MM, where a few million cells are obtainable perpatient biopsy, it is important to minimize the number of cells perexperimental condition, which was in the order of 1,000-10,000 cells inthis assay. The poor clonal efficiency of MM cells, as well as theirspontaneous death in vitro (Suggitt M, Bibby MC. Clinical CancerResearch 2005;11:971-81), suggest that experiments with these samples beperformed in the first few days after the biopsy. By studying the effectof long-term exposure and drug withdrawal in human MM cell lines,mechanistic theoretical models of the drug activity were created(Gardner SN. Cancer Res 2000;60:1417-25). Once a model is generated fora particular drug, the data from patient samples can be used toparameterize and extrapolate the response for longer periods of time.

As shown for bortezomib-induced melphalan sensitization in co-culture(FIG. 6 ), this system can be used to study drug interactions (Chou TC.Pharmacol Rev 2006;58:621-81). The addition of the time dimension,instead of fixed time points, would allow the study of time-shifted drugcombinations, such as, for instance, nuclear export agents anddoxorubicin (Turner JG, Marchion DC, et al. Cancer Res2009;69:6899-905). Combination indices (Chou TC. Pharmacol Rev2006;58:621-81) may be obtained by adding the two drugs being studied onthe same reservoir, which will induce two superimposed drug gradients.

This assay allows the observation of individual cells. Thus, it ispossible to assess the heterogeneity of drug response by plotting in ahistogram the area under the curve (AUC) at the moment of death of eachindividual cell. Further improvements in the digital image analysisalgorithm could identify and track individual cells, from their originalreplication until their death. By combining this information with thedose response surfaces, it would be possible to determine if particulardrugs and concentrations are capable of maintaining a tumor burdenquiescent, or in a balance between proliferation and death (Wells A,Griffith L, et al. Cancer Res 2013;73:3811-6; San-Miguel JF, Mateos MV.Haematol-Hematol J 2011;96:1246-8).

These results describe a framework to better understand the dynamics ofinteractions between tumor and stroma in response to therapeutic agentsin vitro. These assays can be performed in a middle- to high-throughputmanner, and significantly reduce the complexity of working with patientprimary cells in reconstructions of the tumor microenvironment. This canbecome a platform for personalized pre-clinical estimation of drugefficacy in cancer.

Example 2

During a standard-of-care bone marrow biopsy, an extra volume of 10 mLof aspirate was taken for research. The cancer cells were separated fromnon-cancer by magnetic bead sorting (antibody for CD138, a marker of MMcells). Cancer cells from the patient were re-suspended in colagen I ormatrigel or any other matrix of choice in conjunction with stromal cells(adherent non-cancer cells obtained from bone marrow biopsies, CD138-)(FIG. 15A). This cell-matrix mix was seeded in multi-well plates andleft to polymerize overnight. During this process the stromal cellsadhere to the bottom of the wells while MM cells remain in suspension(FIG. 15B). The wells are organized so that multiple drugs can betested, each at a number of different concentrations (e.g., 5) and indifferent number of replicates (e.g, 2 or more) (e.g., FIG. 16 ). Byimaging at regular intervals each well in bright field, and using adigital image analysis algorithm (FIG. 15C), live and dead cells weredetected non-destructively at each well (FIG. 15D). The replicates werethen combined and the results for each drug were clustered, normalizedby the controls (no drugs added) and the dose-response curves were built(Figure 15E).

FIG. 16 displays a schematic of an example multiwell plate used to runmultiple experiments. One sample from a patient (wells in columns 2-8and rows B-L) was tested for sensitivity to 7 drugs: melphalan (MEL),carfilzomib (CFZ), dexamethasone (DEX), doxorubicin (a.k.a. Adriamycin,ADR), Selinexor (KPT), Panobinostat (PAN) and Quisinostat (QST). Thehighest concentrations of drug were on row ‘B’ and are serially diluted3-fold every row from ‘C’ to ‘F’, thus 5 different drug concentrationsfor each drug. The same pattern was repeated from line ‘H’ until ‘L’,representing the second replicate. Squares 114-117 represent thecontrols: the cells in these wells did not receive any drug. Theconcentrations in row ‘M’ are the highest concentration for each drug inthe panel. In the same plate, a second experiment was performed toassess how the microenvironment can affect drug efficacy. For thisexperiment, a multiple myeloma cell line in co-culture with mesenchymalstem cells in collagen matrix (columns 10-16, rows B-E and columns 11and 12 on row G), in single culture in collagen matrix (columns 12, 13,20, and 21 on row G, and columns 10-16 and 18-24 on rows H-L) and insingle culture in media (Columns 18-24, rows B-F, and columns 18 and 19on row G) were used.

The dose-response curves for each patient and each drug (FIG. 17A) werefit to a computational model that describes the rate of accumulation ofdamage due to drug exposure as well as drug-induced cell death due toaccumulated damage (FIG. 17B). The patient-specific model can berepresented by one population (e.g., a perfectly homogeneous tumor), twopopulations or three populations. For instance, if only one population,then the tumor burden will be equal to p1(t); if two populations, thenp1(t)+p2(t); and if three populations, p1(t)+p2(t)+p3(t). Each of thesepopulations can be characterized by a set of parameters ofchemosensitivity to a particular drug or drug combination, as describedin the second equation in (FIG. 17B), namely a_(i) and b_(i). Thus forone population there are two parameters for the model to be fit, a₁ andb₁; for two populations there are 5 parameters, a₁, a₂, b₁, b₂, and so,which is the percentage of the second population at time of biopsy; forthree populations there are 8 parameters: a₁, a₂, a₃, b₁, b₂, b₃, s₀ ands₁, which represent sensitivity parameters of the three populations plusthe percentage at time of biopsy of the second and third populations. APearson correlation of these three hypotheses was used to choose the onewith fewest populations and best fit (highest r^2) (FIG. 17D). Theselected model was then simulated in a clinical regimen of the drug(FIGS. 18-27 ), and two estimates are made: “best case” (Model M-SpikeMax in FIGS. 18-27 ) scenario and “worst case” (Model M-Spike Min inFIGS. 18-27 ) scenarios. In the “worst case” scenario the growth rate is1% for newly diagnosed patients and the highest previous growth rate ofthe tumor for relapsed patients, based on prior clinical data. In the“best case” scenario the growth rate of the tumor is zero for newlydiagnosed patients and the minimum between 1% and “worst case” rate forrelapsed patients.

FIG. 28 displays the Pearson correlation between actual and modelpredictions for normalized tumor burden measurements for 10 MM patientstreated with proteasome inhibitor-based regimens at Moffitt CancerCenter. The dashed square shows that all patients for whom the modelpredicted a clinical response, actually responded, and all thosepredicted not to have a response indeed did not respond. Differentfilled in circles represent the interval of time after biopsy when eachtumor measurement of made: less than a month (light grey), between oneand two months (white), and over two months (dark grey).

FIG. 29 displays the actual and estimated normalized tumor burden formultiple myeloma patients treated in proteasome inhibitor-basedregimens. 10 multiple myeloma patients who donated bone marrow aspiratesfor the assay described herein were followed after treatment. Each entryin the column ‘Time (months)’ represents the delay (in months) betweenthe tumor burden measurement and the original biopsy. Column ‘ClinicalBurden (% original)’ represents the tumor burden measurement at thatparticular moment in time normalized by the tumor burden at the time ofbiopsy. ‘Mean’ is the average between the model estimations for best(‘Min’) and worst (‘Max’) case scenarios, which correspond to smallestand largest tumor estimation. ‘Treatment’ represents the actual clinicaltreatment received by the patient. ‘Drug Ex vivo’ represents the drugused to test the sensitivity of the cells of these patients and createthe estimations of clinical response. While these patients have beentested ex vivo for one particular proteasome inhibitor (bortezomib),these models were able to reliably estimate clinical response ofpatients treated with different proteasome inhibitor drugs as singleagents (phase I trials) or in combination with other drugs (IMIDS).

Unless defined otherwise, all technical and scientific terms used hereinhave the same meanings as commonly understood by one of skill in the artto which the disclosed invention belongs. Publications cited herein andthe materials for which they are cited are specifically incorporated byreference.

Those skilled in the art will recognize, or be able to ascertain usingno more than routine experimentation, many equivalents to the specificembodiments of the invention described herein. Such equivalents areintended to be encompassed by the following claims.

What is claimed is: 1-29. (canceled)
 30. A method for selecting a cancertreatment regimen for a subject, comprising: (a) administering cancercells from the subject to a microfluidic chamber that recapitulates thecancer microenvironment and comprises a linear drug gradient across thechamber; (b) identifying cell death induced by the drug across the druggradient at one or more time points; (c) collecting parameters from theassay to generate a multi-parameter model that summarizes the responseof the subject to the drug treatment; and (d) selecting a cancertreatment regimen for the subject based on the results of themulti-parameter model.
 31. The method of claim 30, wherein themicrofluidic chamber comprises extracellular matrix, subject-derivedstroma, and growth factors to recapitulate the cancer microenvironment.32. The method of claim 30, wherein step (b) comprises: (a) collecting afirst bright field image of a cancer cell at a first time; (b)collecting a second bright field image of a cancer cell at a secondtime; and (c) applying an algorithm to the first and second images toidentify the presence or absence of cell membrane motion; wherein theabsence of cell membrane motion indicates cell death.
 33. The method ofclaim 30, wherein less than 20,000 cancer cells are used for the assay.34. The method of claim 30, wherein only bright field imaging is used toidentify cell death.
 35. The method of claim 30, wherein cell death isidentified at two or more time points for the same cancer cells.
 36. Themethod of claim 30, wherein the method predicts the initial response toa drug.
 37. The method of claim 30, wherein the method predicts thechance of progression-free survival.
 38. The method of claim 30, whereinthe assay allows for assessment of environment-mediated drug resistance.39. The method of claim 30, wherein a combination of drugs is tested.40. The method of claim 30, wherein a dosing schedule of the drug istested.
 41. The method of claim 30, wherein the cancer is ahematological cancer.
 42. The method of claim 30, wherein the cancer ismultiple myeloma.
 43. The method of claim 30, wherein the sample is abone marrow aspirate.
 44. The method of claim 30, wherein the drugcomprises melphalan, bortezomib, FAM-HYD-1, or combinations thereof.